ScISI                 package:ScISI                 R Documentation

_T_h_e _I_n _S_i_l_i_c_o _I_n_t_e_r_a_c_t_o_m_e _f_o_r _S_a_c_c_h_a_r_o_m_y_c_e_s _c_e_r_e_v_i_s_i_a_e

_D_e_s_c_r_i_p_t_i_o_n:

     This is the incidence sparse-matrix representatin for the
     bi-partite graph for the in silico interactome given by
     Saccharomyces cerevisiae. The rows are indexed by the systematic
     gene names and the colunmns are indexed by the protein complexes.
     This matrix contains a 1 in the (i,j) postion if the protein in
     indexed in the i-th row is a member of the protein complex of the
     j-th column; it contains a 0 otherwise.

     ScISIC is a sub-interactome of ScISI which consists of protein
     complexes derived from small scale experiments and have been
     curated by Gene Ontology (GO) or MIPS. While these complexes have
     been curated, not all of them have been completely verified to be
     true. Periodic changes to GO and MIPS  will percolate through the
     protein complexes or protein complex composition and so the ScISIC
     will need to be rebuilt. A script located in the  inst/Scripts/
     entitled createScISIC.R creates an updated ScISIC if the GO and
     MIPS's files are up to date. GO 2.0.0 and complexcat-data-2006
     (MIPS) were  used to build ScISIC for Bioconductor 2.1 release of
     the package ScISI. Both are  the most up to date versions of the
     repository as of 9 October 2007. In addition to MIPS and GO, we
     have also incorporated protein complexes curated by the  IntAct
     repository. The IntAct protein complexes are obtained from the 
     complex data XML file obtained from IntAct via Rintact. 

     In addition to the protein complexes found within MIPS and GO,
     ScISIC also contains manually curated protein complexes obtained
     from IntAct. Because IntAct has yet to version its release, the
     protein complexes were obtained on 25 May 2007. 

     ScISIC replaces ScISIverified which has been deprecated.

     ScISI combines ScISIC with protein complex estimates on the
     datasets derived by Gavin et al (2002), Ho et al (2002), and
     Krogan et al (2004) using the penalized algorithm found with
     apComplex developed by Scholtens et al (2004).

_U_s_a_g_e:

     data(ScISI)

_F_o_r_m_a_t:

     The format of both the ScISI and ScISIC is a binary incidence
     matrix.  The rows  are indexed by the gene locus names and the
     columns are indexed by the  identification codes for the protein
     complexes based on the repository from where they are obtained.

_D_e_t_a_i_l_s:

     This is the working in silico interactome built for computational
     experimentation. The data from which this interactome is built is
     from the Intact, Gene Ontology, Mips, and estimated protein
     complexes from apComplex.

_S_o_u_r_c_e:

     http://www.geneontology.org

_R_e_f_e_r_e_n_c_e_s:

     http://www/bioconductor.org

_E_x_a_m_p_l_e_s:

     data(ScISIC)

